Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 20 of 255
Found at i:5348803 original size:17 final size:18
Alignment explanation
Indices: 5348781--5348814 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5348771 AATCTGGACA
5348781 TGTGGG-CCACACGGGCG
1 TGTGGGTCCACACGGGCG
*
5348798 TGTGGGTCTACACGGGC
1 TGTGGGTCCACACGGGC
5348815 AGACCACATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.18
Consensus pattern (18 bp):
TGTGGGTCCACACGGGCG
Found at i:5353847 original size:13 final size:13
Alignment explanation
Indices: 5353831--5353856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5353821 CTCAATCAAT
5353831 AACAAAAAAAAAA
1 AACAAAAAAAAAA
5353844 AACAAAAAAAAAA
1 AACAAAAAAAAAA
5353857 CGAAAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AACAAAAAAAAAA
Found at i:5353852 original size:11 final size:11
Alignment explanation
Indices: 5353836--5353873 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
5353826 TCAATAACAA
5353836 AAAAAAAAAAC
1 AAAAAAAAAAC
5353847 AAAAAAAAAAC
1 AAAAAAAAAAC
*
5353858 GAAAACAAAAAC
1 -AAAAAAAAAAC
5353870 AAAA
1 AAAA
5353874 TTTTTTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:5353852 original size:12 final size:12
Alignment explanation
Indices: 5353835--5353873 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5353825 ATCAATAACA
5353835 AAAAAAAAAAAC
1 AAAAAAAAAAAC
5353847 -AAAAAAAAAAC
1 AAAAAAAAAAAC
* *
5353858 GAAAACAAAAAC
1 AAAAAAAAAAAC
5353870 AAAA
1 AAAA
5353874 TTTTTTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:5353856 original size:17 final size:17
Alignment explanation
Indices: 5353834--5353873 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5353824 AATCAATAAC
5353834 AAAAAAAAAAAACAAAA
1 AAAAAAAAAAAACAAAA
**
5353851 AAAAAACGAAAACAAAA
1 AAAAAAAAAAAACAAAA
5353868 ACAAAA
1 A-AAAA
5353874 TTTTTTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.88, C:0.10, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAACAAAA
Found at i:5354447 original size:15 final size:15
Alignment explanation
Indices: 5354427--5354457 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5354417 AAAACAATAT
5354427 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
5354442 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
5354457 A
1 A
5354458 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:5357829 original size:15 final size:15
Alignment explanation
Indices: 5357819--5357848 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5357809 TCCCTTCTTG
5357819 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
5357834 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
5357849 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:5358616 original size:17 final size:18
Alignment explanation
Indices: 5358590--5358628 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5358580 CAAATTGTGG
5358590 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
5358606 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
5358624 AAAAT
1 AAAAT
5358629 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:5358805 original size:15 final size:15
Alignment explanation
Indices: 5358785--5358815 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5358775 AAAACAATAT
5358785 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
5358800 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
5358815 A
1 A
5358816 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:5365658 original size:21 final size:21
Alignment explanation
Indices: 5365634--5365677 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5365624 TTATCTTTTA
5365634 TTTGGACTTTATTTTGGAGTT
1 TTTGGACTTTATTTTGGAGTT
5365655 TTTGGACTTTATTTTGGAGTT
1 TTTGGACTTTATTTTGGAGTT
5365676 TT
1 TT
5365678 CGCATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.05, G:0.23, T:0.59
Consensus pattern (21 bp):
TTTGGACTTTATTTTGGAGTT
Found at i:5369492 original size:22 final size:23
Alignment explanation
Indices: 5369450--5369492 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5369440 TTCTTTTATA
*
5369450 TATAACAATATACTTTTATATTC
1 TATAACAATATACTTTAATATTC
*
5369473 TATAA-AATATAGTTTAATAT
1 TATAACAATATACTTTAATAT
5369493 GCAATAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TATAACAATATACTTTAATATTC
Found at i:5369499 original size:22 final size:23
Alignment explanation
Indices: 5369451--5369499 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
5369441 TCTTTTATAT
* * *
5369451 ATAACAATATACTTTTATATTCT
1 ATAACAATATACTTTAATATGCA
*
5369474 ATAA-AATATAGTTTAATATGCA
1 ATAACAATATACTTTAATATGCA
5369496 ATAA
1 ATAA
5369500 TCTTACTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (23 bp):
ATAACAATATACTTTAATATGCA
Found at i:5374773 original size:46 final size:46
Alignment explanation
Indices: 5374685--5374950 Score: 325
Period size: 46 Copynumber: 6.0 Consensus size: 46
5374675 TTTGACGTGA
* * * * * * *
5374685 TGCCATAGTGTCTTTCAACTATGGTTTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
5374731 TTCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5374777 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5374823 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5374869 TGTCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5374907 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5374951 AGAGCACACT
Statistics
Matches: 193, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
38 32 0.17
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 147 0.76
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:5374915 original size:38 final size:38
Alignment explanation
Indices: 5374864--5374939 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
5374854 CATTTCATAT
*
5374864 CAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5374902 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5374940 TTTCATATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:5376826 original size:17 final size:17
Alignment explanation
Indices: 5376804--5376838 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5376794 ATACTTACCT
5376804 TGTTCTATTGATACTAA
1 TGTTCTATTGATACTAA
5376821 TGTTCTATTGATACTAA
1 TGTTCTATTGATACTAA
5376838 T
1 T
5376839 CTTTAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TGTTCTATTGATACTAA
Found at i:5377153 original size:31 final size:32
Alignment explanation
Indices: 5377096--5377175 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
5377086 CTTTATATAC
*
5377096 TAATAAAATAATAAAATATCTTATTAAAGT-AT
1 TAATAAAATAATAAAATATCTAATTAAA-TAAT
**
5377128 TAATAAAATAAT-ATTTATCTAATTAAATAAT
1 TAATAAAATAATAAAATATCTAATTAAATAAT
5377159 T-ATAAAAT-ATCAAAATA
1 TAATAAAATAAT-AAAATA
5377176 CCTCTAGCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
29 2 0.05
30 8 0.20
31 18 0.45
32 12 0.30
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (32 bp):
TAATAAAATAATAAAATATCTAATTAAATAAT
Found at i:5380662 original size:28 final size:27
Alignment explanation
Indices: 5380616--5380669 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
5380606 TCGACGACCG
*
5380616 ATAAAAAAATAAAAGAGAAACAAGAAAA
1 ATAAAAAAATAAAAAAGAAA-AAGAAAA
5380644 ATAAAAAAA-AAGAAAAGAAAAAGAAA
1 ATAAAAAAATAA-AAAAGAAAAAGAAA
5380670 TTGAGGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (27 bp):
ATAAAAAAATAAAAAAGAAAAAGAAAA
Found at i:5380664 original size:11 final size:11
Alignment explanation
Indices: 5380637--5380669 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5380627 AAAGAGAAAC
*
5380637 AAGAAAAATAA
1 AAGAAAAAGAA
5380648 AA-AAAAAGAA
1 AAGAAAAAGAA
5380658 AAGAAAAAGAA
1 AAGAAAAAGAA
5380669 A
1 A
5380670 TTGAGGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:5384145 original size:29 final size:29
Alignment explanation
Indices: 5384070--5384182 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 29
5384060 TACATACATG
* * *
5384070 CATATAGCCCACTAGGCTCAATCTCAT--T
1 CATATGGCCCACTACGCCCAAT-TCATACT
* *
5384098 CATATGGCCTATCT-GGCCCAATTCATACT
1 CATATGGCCCA-CTACGCCCAATTCATACT
* * *
5384127 CTTATGGCCCACTACGCCCAATTCACATT
1 CATATGGCCCACTACGCCCAATTCATACT
* * *
5384156 CATATGGCCCATTAGGCCCAAATCATA
1 CATATGGCCCACTACGCCCAATTCATA
5384183 GTATACTCAT
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.06
28 18 0.26
29 46 0.68
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (29 bp):
CATATGGCCCACTACGCCCAATTCATACT
Found at i:5384279 original size:18 final size:19
Alignment explanation
Indices: 5384256--5384293 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5384246 ATGGGCCCGA
5384256 TAGCCCA-TCAGGCCCATT
1 TAGCCCATTCAGGCCCATT
*
5384274 TAGCCCATTCCGGCCCATT
1 TAGCCCATTCAGGCCCATT
5384293 T
1 T
5384294 GGCCAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.39, G:0.16, T:0.26
Consensus pattern (19 bp):
TAGCCCATTCAGGCCCATT
Found at i:5384302 original size:19 final size:19
Alignment explanation
Indices: 5384266--5384302 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5384256 TAGCCCATCA
*
5384266 GGCCCATTTAGCCCATTCC
1 GGCCCATTTAGCCAATTCC
*
5384285 GGCCCATTTGGCCAATTC
1 GGCCCATTTAGCCAATTC
5384303 TCAACCCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.38, G:0.19, T:0.27
Consensus pattern (19 bp):
GGCCCATTTAGCCAATTCC
Found at i:5385698 original size:16 final size:16
Alignment explanation
Indices: 5385674--5385705 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5385664 AAGTTCGGGA
5385674 TTTCAGGATTTTTGGG
1 TTTCAGGATTTTTGGG
*
5385690 TTTCGGGATTTTTGGG
1 TTTCAGGATTTTTGGG
5385706 GGCGTTACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (16 bp):
TTTCAGGATTTTTGGG
Found at i:5387434 original size:17 final size:19
Alignment explanation
Indices: 5387412--5387452 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5387402 CATAAAGATA
5387412 AAACT-AAATAAAAACTG-
1 AAACTAAAATAAAAACTGT
*
5387429 AAACTAAAATAAAATCTGT
1 AAACTAAAATAAAAACTGT
5387448 AAACT
1 AAACT
5387453 CTAGGTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 11 0.52
19 5 0.24
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (19 bp):
AAACTAAAATAAAAACTGT
Found at i:5389019 original size:6 final size:6
Alignment explanation
Indices: 5388986--5389029 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
5388976 TACACTTAGT
* * *
5388986 TTCAGT TTCAGA TTTAGA TATCATA TTCAGA TTCAGA TTCAGA T
1 TTCAGA TTCAGA TTCAGA T-TCAGA TTCAGA TTCAGA TTCAGA T
5389030 AGCAGATATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (6 bp):
TTCAGA
Found at i:5389584 original size:31 final size:31
Alignment explanation
Indices: 5389542--5389618 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
5389532 GCCCCAAAAT
5389542 CCACACGCCCGTGTGACATACCCGTGTGGGC
1 CCACACGCCCGTGTGACATACCCGTGTGGGC
* * *
5389573 CCACACACCCGTGTGACATGCCTGTGTGGGC
1 CCACACGCCCGTGTGACATACCCGTGTGGGC
*
5389604 CCACACGCTCGTGTG
1 CCACACGCCCGTGTG
5389619 GCACACACGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.16, C:0.38, G:0.29, T:0.18
Consensus pattern (31 bp):
CCACACGCCCGTGTGACATACCCGTGTGGGC
Found at i:5396104 original size:32 final size:33
Alignment explanation
Indices: 5396032--5396105 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
5396022 AAGGGTAGTA
* * * *
5396032 TTGAAAAGGAAAGGTATACTTTGTGTATACCAC
1 TTGAAAAGGAAAAGTACACTATATGTATACCAC
* *
5396065 TTAAAAAGGAAAAGTACACTATATGTGTA-CAC
1 TTGAAAAGGAAAAGTACACTATATGTATACCAC
5396097 TTGAAAAGG
1 TTGAAAAGG
5396106 TTATGTGCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 11 0.32
33 23 0.68
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (33 bp):
TTGAAAAGGAAAAGTACACTATATGTATACCAC
Found at i:5396158 original size:33 final size:33
Alignment explanation
Indices: 5396089--5396169 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
5396079 TACACTATAT
** * **
5396089 GTGTA-CACTTGAAAAGGTTATGTGCACTTCGT
1 GTGTACCACTTGAAAAGGGAATGTGCACCTCAA
5396121 GTGTACCACTTGAAAAGGGAATGTGCACCTCAA
1 GTGTACCACTTGAAAAGGGAATGTGCACCTCAA
* *
5396154 GTGTACAACTAGAAAA
1 GTGTACCACTTGAAAA
5396170 AGACAGGTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 5 0.12
33 36 0.88
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (33 bp):
GTGTACCACTTGAAAAGGGAATGTGCACCTCAA
Found at i:5398469 original size:14 final size:15
Alignment explanation
Indices: 5398450--5398486 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5398440 ATGGAATTTT
*
5398450 ATTAAAAATTA-AGA
1 ATTAAAAATTAGAAA
5398464 ATTAAAAA-TAGAAA
1 ATTAAAAATTAGAAA
5398478 ATTAAAAAT
1 ATTAAAAAT
5398487 GGAGGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (15 bp):
ATTAAAAATTAGAAA
Found at i:5398756 original size:17 final size:18
Alignment explanation
Indices: 5398731--5398766 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5398721 AAAATCACCC
5398731 TAATATAATTT-ATTTTT
1 TAATATAATTTAATTTTT
*
5398748 TAATTTAATTTAATTTTT
1 TAATATAATTTAATTTTT
5398766 T
1 T
5398767 TAAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATATAATTTAATTTTT
Found at i:5402969 original size:22 final size:22
Alignment explanation
Indices: 5402941--5402982 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5402931 TATAGTGTAA
*
5402941 AAAATATATACATAATATAATT
1 AAAATATATACATAAGATAATT
5402963 AAAATATATACATAAGATAA
1 AAAATATATACATAAGATAA
5402983 CATGTAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATATATACATAAGATAATT
Found at i:5403034 original size:25 final size:25
Alignment explanation
Indices: 5402998--5403133 Score: 95
Period size: 25 Copynumber: 5.6 Consensus size: 25
5402988 AGGAAAAAAT
*
5402998 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
5403023 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAGTATTAA-AG
* * * *
5403048 ATATATACGTAATGTAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
5403072 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* * *
5403094 AATATATATATAATATAATATTAAAA
1 -ATATATACATAATATAGTATTAAAG
5403120 ATATAATA-ATAATA
1 ATAT-ATACATAATA
5403134 ATAAAAAAGA
Statistics
Matches: 85, Mismatches: 18, Indels: 16
0.71 0.15 0.13
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 13 0.15
24 17 0.20
25 44 0.52
26 8 0.09
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:5403133 original size:20 final size:19
Alignment explanation
Indices: 5403101--5403140 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
5403091 AAGAATATAT
*
5403101 ATATAATATAATATTAAAA
1 ATATAATATAATAATAAAA
5403120 ATATAATAATAATAATAAAA
1 ATATAAT-ATAATAATAAAA
5403140 A
1 A
5403141 AGAGAAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAATATAATAATAAAA
Found at i:5403136 original size:14 final size:14
Alignment explanation
Indices: 5403103--5403136 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5403093 GAATATATAT
*
5403103 ATAATATAATATTA
1 ATAATATAATAATA
*
5403117 AAAATATAATAATA
1 ATAATATAATAATA
5403131 ATAATA
1 ATAATA
5403137 AAAAAGAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATATAATAATA
Found at i:5404785 original size:19 final size:19
Alignment explanation
Indices: 5404761--5404798 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5404751 CTACAGAGGC
*
5404761 GTCCTTATTTTCGAAACAT
1 GTCCTTATTTCCGAAACAT
5404780 GTCCTTATTTCCGAAACAT
1 GTCCTTATTTCCGAAACAT
5404799 ATCTTTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (19 bp):
GTCCTTATTTCCGAAACAT
Found at i:5406078 original size:58 final size:58
Alignment explanation
Indices: 5405988--5406104 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
5405978 GAAGGCTTCA
5405988 GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
1 GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
*
5406046 GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTTTTGAGCCTCGT
1 GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
5406104 G
1 G
5406105 ATCATCTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.14, C:0.30, G:0.15, T:0.42
Consensus pattern (58 bp):
GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
Found at i:5408579 original size:23 final size:22
Alignment explanation
Indices: 5408553--5408596 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
5408543 ATAAATAGTA
5408553 ATAGTGTTAGAAATATACTATAT
1 ATAGTGTTAGAAATATA-TATAT
* *
5408576 ATAGTGTTTGAAGTATATATA
1 ATAGTGTTAGAAATATATATA
5408597 GAAAATAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (22 bp):
ATAGTGTTAGAAATATATATAT
Found at i:5408654 original size:25 final size:26
Alignment explanation
Indices: 5408625--5408677 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
5408615 ACTAGTAATG
*
5408625 TACATAATATAGTATAAAA-A-ATACA
1 TACATAATATAAT-TAAAATATATACA
5408650 TACATAATATAATTAAAATATATACA
1 TACATAATATAATTAAAATATATACA
5408676 TA
1 TA
5408678 AAATAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 13 0.52
26 7 0.28
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (26 bp):
TACATAATATAATTAAAATATATACA
Found at i:5408674 original size:22 final size:22
Alignment explanation
Indices: 5408642--5408683 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5408632 TATAGTATAA
*
5408642 AAAATACATACATAATATAATT
1 AAAATACATACATAAAATAATT
*
5408664 AAAATATATACATAAAATAA
1 AAAATACATACATAAAATAA
5408684 CATGTGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATACATACATAAAATAATT
Found at i:5408725 original size:15 final size:14
Alignment explanation
Indices: 5408694--5408754 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
5408684 CATGTGGAAA
5408694 AAATATATATATAT
1 AAATATATATATAT
5408708 AAATA-ATATAGTATT
1 AAATATATATA-TA-T
* *
5408723 AAAGATATATACAT
1 AAATATATATATAT
5408737 AAAATAGTATAATATAT
1 -AAATA-TAT-ATATAT
5408754 A
1 A
5408755 TACGTAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
13 5 0.14
14 8 0.22
15 10 0.27
16 9 0.24
17 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:5408730 original size:25 final size:25
Alignment explanation
Indices: 5408702--5408825 Score: 100
Period size: 23 Copynumber: 5.2 Consensus size: 25
5408692 AAAAATATAT
*
5408702 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
5408727 ATATATACATAAAATAGTA-T-AAT
1 ATATATACATAATATAGTATTAAAG
* * *
5408750 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
5408774 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* *
5408796 A-ATATATATAATATAATATTAAAAG
1 ATATATACATAATATAGTATT-AAAG
5408821 ATATA
1 ATATA
5408826 ATAATAACAA
Statistics
Matches: 78, Mismatches: 15, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.01
22 15 0.19
23 32 0.41
24 5 0.06
25 22 0.28
26 3 0.04
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:5408755 original size:48 final size:48
Alignment explanation
Indices: 5408700--5408825 Score: 123
Period size: 48 Copynumber: 2.7 Consensus size: 48
5408690 GAAAAAATAT
*
5408700 ATATATATAAATAATATAGTATTAAAGATATATACATAAAATAGTATA
1 ATATATATAAATAATATAGTATTAAAGATATATACATAAAATAGTAAA
** * * * * *
5408748 ATATATATACGTAATATAGAATT-TAGA-ATATACCTAATATATTAAA
1 ATATATATAAATAATATAGTATTAAAGATATATACATAAAATAGTAAA
* * *
5408794 AGA-ATATATATAATATAATATTAAAAGATATA
1 ATATATATAAATAATATAGTATT-AAAGATATA
5408826 ATAATAACAA
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
45 15 0.25
46 17 0.28
47 6 0.10
48 23 0.38
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (48 bp):
ATATATATAAATAATATAGTATTAAAGATATATACATAAAATAGTAAA
Found at i:5409143 original size:15 final size:16
Alignment explanation
Indices: 5409108--5409146 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
5409098 TAATCTCCAA
*
5409108 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
5409124 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
5409140 AAAAACT
1 AAAAACT
5409147 CTTCTCCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.05, T:0.21
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:5415334 original size:2 final size:2
Alignment explanation
Indices: 5415327--5415351 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5415317 CTTCTCTTTT
5415327 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5415352 TAAAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5417800 original size:3 final size:3
Alignment explanation
Indices: 5417792--5417825 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5417782 AAAAAGGACC
5417792 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5417826 TTGGTTCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5419934 original size:30 final size:30
Alignment explanation
Indices: 5419900--5419957 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5419890 TTTAACAAGC
*
5419900 AAATGCCTCTAGAATAATAACAAAATTAGG
1 AAATGCCTCTAAAATAATAACAAAATTAGG
* * *
5419930 AAATGTCTTTAAAATAATAATAAAATTA
1 AAATGCCTCTAAAATAATAACAAAATTA
5419958 ATAATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAGG
Found at i:5419961 original size:12 final size:12
Alignment explanation
Indices: 5419939--5419967 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5419929 GAAATGTCTT
5419939 TAAAA-TAATAA
1 TAAAATTAATAA
5419950 TAAAATTAATAA
1 TAAAATTAATAA
5419962 TAAAAT
1 TAAAAT
5419968 AAGTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:5420016 original size:22 final size:22
Alignment explanation
Indices: 5419991--5420033 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5419981 TATCCAAACA
5419991 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
5420013 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
5420034 AATAGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:5420037 original size:11 final size:11
Alignment explanation
Indices: 5419998--5420038 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5419988 ACAATAACAA
5419998 CAAAATAGTAG
1 CAAAATAGTAG
* *
5420009 CAACATAATAG
1 CAAAATAGTAG
*
5420020 TAAAATAGTAG
1 CAAAATAGTAG
5420031 CAAAATAG
1 CAAAATAG
5420039 GGAAAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:5427342 original size:18 final size:18
Alignment explanation
Indices: 5427300--5427345 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5427290 TAAGCCCCCT
*
5427300 CCCAAAAAAACTTAACCC
1 CCCAAAAAAACCTAACCC
***
5427318 AAAAAAAAAACCTAACCC
1 CCCAAAAAAACCTAACCC
5427336 CCCAAAAAAA
1 CCCAAAAAAA
5427346 AACCAAGAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.61, C:0.33, G:0.00, T:0.07
Consensus pattern (18 bp):
CCCAAAAAAACCTAACCC
Found at i:5431353 original size:12 final size:12
Alignment explanation
Indices: 5431336--5431371 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5431326 AACATTTTGA
5431336 CATTCATACATT
1 CATTCATACATT
**
5431348 CATTCATGTATT
1 CATTCATACATT
5431360 CATTCATACATT
1 CATTCATACATT
5431372 GCATATCCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (12 bp):
CATTCATACATT
Found at i:5439873 original size:116 final size:116
Alignment explanation
Indices: 5439652--5439957 Score: 524
Period size: 116 Copynumber: 2.6 Consensus size: 116
5439642 GTTGAGGTAT
* * * * *
5439652 TTTTAATTGTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGTCTAGGGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
5439716 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAAAGGTGAGTTAAGCC
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAAAGGTGAGTTAAGCC
5439767 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
* *
5439832 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCTAGAGGTGAGTTAAGCC
66 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAAAGGTGAGTTAAGCC
* *
5439883 TTTTTATTTTGGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
5439948 GAGGTATTTT
66 GAGGTATTTT
5439958 CAATTTTTGT
Statistics
Matches: 181, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
115 11 0.06
116 170 0.94
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (116 bp):
TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAAAGGTGAGTTAAGCC
Found at i:5440005 original size:72 final size:73
Alignment explanation
Indices: 5439888--5440077 Score: 233
Period size: 72 Copynumber: 2.6 Consensus size: 73
5439878 AAGCCTTTTT
* * * * * *
5439888 ATTTTGGTTTTTCAA-AATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGG
1 ATTTTTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGG
*
5439952 TATTTTCA
66 TAATTTCA
* ** * *
5439960 ATTTTTGTGTT-TTAA-TTTCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACAGGATGAG
1 ATTTTTGT-TTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAG
5440023 GTAATTTCA
65 GTAATTTCA
*
5440032 ATTTTTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 ATTTTTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGA
5440078 ACCTTTTAAT
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
71 2 0.02
72 69 0.70
73 28 0.28
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (73 bp):
ATTTTTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGG
TAATTTCA
Found at i:5440377 original size:55 final size:56
Alignment explanation
Indices: 5440317--5440437 Score: 165
Period size: 56 Copynumber: 2.2 Consensus size: 56
5440307 TGAGGTATTC
* * * *
5440317 TTAATTTTTGTTGTTT-CAAAAA-TCAACTCATGTTGCGAGAGGTGAGTTAAGCCTT
1 TTAATTTCTGTT-TTTAAAAAAATTCAACTCATATTGCAAGAGGTGAGTTAAGCCTT
* *
5440372 TTAATTTCTGTTTTTAAAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCTTT
1 TTAATTTCTGTTTTTAAAAAAATTCAACTCATATTGCAAGAGGTGAGTTAAGCCTT
5440428 TTAATTTCTG
1 TTAATTTCTG
5440438 CGAGAGTTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
54 3 0.05
55 16 0.28
56 39 0.67
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (56 bp):
TTAATTTCTGTTTTTAAAAAAATTCAACTCATATTGCAAGAGGTGAGTTAAGCCTT
Found at i:5440451 original size:30 final size:30
Alignment explanation
Indices: 5440410--5440467 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
5440400 TCATATTGCA
5440410 AGAGGTGAGTTGAG-CTTTTTAATTTCTGCG
1 AGAGGTGAGTTGAGTC-TTTTAATTTCTGCG
*
5440440 AGAGTTGAGTTGAGTCTTTTAATTTCTG
1 AGAGGTGAGTTGAGTCTTTTAATTTCTG
5440468 TTTTTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.43
Consensus pattern (30 bp):
AGAGGTGAGTTGAGTCTTTTAATTTCTGCG
Found at i:5443228 original size:12 final size:12
Alignment explanation
Indices: 5443211--5443235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5443201 AACATAAAAG
5443211 ATTTATTTATTA
1 ATTTATTTATTA
5443223 ATTTATTTATTA
1 ATTTATTTATTA
5443235 A
1 A
5443236 GTACGTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTATTA
Found at i:5444405 original size:49 final size:49
Alignment explanation
Indices: 5444349--5444448 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
5444339 AATAGGGCAT
5444349 GGACATTGACACTATGATGGGTTATGTCTTATGGAATTACTATATAAAA
1 GGACATTGACACTATGATGGGTTATGTCTTATGGAATTACTATATAAAA
*
5444398 GGACATTGACACTATGATGGGTTATGTCTTATGGATTTACTATATAAAA
1 GGACATTGACACTATGATGGGTTATGTCTTATGGAATTACTATATAAAA
5444447 GG
1 GG
5444449 CCCTCGGTCC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (49 bp):
GGACATTGACACTATGATGGGTTATGTCTTATGGAATTACTATATAAAA
Found at i:5448446 original size:3 final size:3
Alignment explanation
Indices: 5448440--5448475 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
5448430 TTGTTTTTTT
* *
5448440 TAA TAA TAA TAA TAA TAA TGA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5448476 ATATTATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5448789 original size:22 final size:22
Alignment explanation
Indices: 5448764--5448821 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
5448754 TGATATTAGT
*
5448764 AATAAAAAATAATAGCTATAAA
1 AATAAAAAATAATAGCCATAAA
* * *
5448786 AAT-AAAAATAATAACCATGAC
1 AATAAAAAATAATAGCCATAAA
*
5448807 AATAAAGAATAATAG
1 AATAAAAAATAATAG
5448822 TAATAATAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
AATAAAAAATAATAGCCATAAA
Found at i:5449258 original size:28 final size:28
Alignment explanation
Indices: 5449200--5449261 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
5449190 AACGCCAATG
* * *
5449200 ATAATATTAATATTGATAATAAATAATA
1 ATAATATAAACATTGATAATAAATAAAA
*
5449228 ATAATATAAACATTGATGAT-AATAGAAA
1 ATAATATAAACATTGATAATAAATA-AAA
5449256 ATAATA
1 ATAATA
5449262 ATGTTAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (28 bp):
ATAATATAAACATTGATAATAAATAAAA
Found at i:5460416 original size:20 final size:20
Alignment explanation
Indices: 5460391--5460433 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
5460381 AAACACTACC
5460391 TTTCAATATTTATATAATCA
1 TTTCAATATTTATATAATCA
5460411 TTTCAATATTTATATAATCA
1 TTTCAATATTTATATAATCA
5460431 TTT
1 TTT
5460434 ACATAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTCAATATTTATATAATCA
Found at i:5460999 original size:82 final size:81
Alignment explanation
Indices: 5460862--5461024 Score: 265
Period size: 82 Copynumber: 2.0 Consensus size: 81
5460852 AGCAAATCTA
*
5460862 AATAAACATAGTGTTAATATTCTATCATCAATAAATTTTTACTTTACTTTATCATCCCGAGTTGC
1 AATAAACATAGTGTTAATATTCTATCATCAATAAATTTTTACTTTACTTTATCATCCCAAGTTGC
5460927 CAAACAATGATGGATT
66 CAAACAATGATGGATT
* *
5460943 AATAAACATATTGTGTTAATATTCTATCATCAAT-AATTTTTAGTTTACTTTGTCATCCCAAGTT
1 AATAAACATA--GTGTTAATATTCTATCATCAATAAATTTTTACTTTACTTTATCATCCCAAGTT
*
5461007 GCCTAACAATGATGGATT
64 GCCAAACAATGATGGATT
5461025 TCATTGATAT
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
81 10 0.13
82 44 0.58
83 22 0.29
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (81 bp):
AATAAACATAGTGTTAATATTCTATCATCAATAAATTTTTACTTTACTTTATCATCCCAAGTTGC
CAAACAATGATGGATT
Found at i:5462586 original size:25 final size:25
Alignment explanation
Indices: 5462568--5462629 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
5462558 AATTTACTTA
*
5462568 TATATTTA-TTGATTTAATTCTAAT
1 TATAATTATTTGATTTAATTCTAAT
*
5462592 TCTAATTATTTGATTTAATTCTAAT
1 TATAATTATTTGATTTAATTCTAAT
5462617 TATAATTATTTGA
1 TATAATTATTTGA
5462630 ATATATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 6 0.18
25 28 0.82
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (25 bp):
TATAATTATTTGATTTAATTCTAAT
Found at i:5466563 original size:33 final size:33
Alignment explanation
Indices: 5466516--5466580 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
5466506 CATACCTGTG
*
5466516 TGGCCCACATGGCCCAAATTGGCCTTGACCGTA
1 TGGCCCACACGGCCCAAATTGGCCTTGACCGTA
5466549 TGGCCCACACGGCCCAAATTGGCCTTGACCGT
1 TGGCCCACACGGCCCAAATTGGCCTTGACCGT
5466581 GTGGAACACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (33 bp):
TGGCCCACACGGCCCAAATTGGCCTTGACCGTA
Found at i:5468478 original size:62 final size:60
Alignment explanation
Indices: 5468409--5468567 Score: 142
Period size: 62 Copynumber: 2.6 Consensus size: 60
5468399 TAATTTATAT
* ** *
5468409 TTTATGTATAATTATATTAAATTATTTAAATATTATTTATTA-TATTTAAAATTTTAAAATA
1 TTTATGTATAATTATATTAAATTATTTAAATATTATTAAAAAGTATTTAAAA-TAT-AAATA
* * * ** * *
5468470 TTTCATGTAGAATTAAATTTACAAATAAATAATTAATTATTAAAAAGTATTTAAAATATATATA
1 TTT-ATGTATAATTATA-TTA-AATTATTTAAAT-ATTATTAAAAAGTATTTAAAATATAAATA
*
5468534 -TTATGTATAATTATATTAGATTATTTAAATATTA
1 TTTATGTATAATTATATTAAATTATTTAAATATTA
5468568 ACTAATTTAA
Statistics
Matches: 75, Mismatches: 18, Indels: 12
0.71 0.17 0.11
Matches are distributed among these distances:
59 4 0.05
60 7 0.09
61 6 0.08
62 22 0.29
63 5 0.07
64 12 0.16
65 10 0.13
66 9 0.12
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (60 bp):
TTTATGTATAATTATATTAAATTATTTAAATATTATTAAAAAGTATTTAAAATATAAATA
Found at i:5470316 original size:23 final size:23
Alignment explanation
Indices: 5470285--5470335 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
5470275 TCTTATAAGC
*
5470285 AATTGAATGAATATATTCAATTA
1 AATTAAATGAATATATTCAATTA
5470308 AATTAAATGAATATATTCAATTA
1 AATTAAATGAATATATTCAATTA
5470331 AATTA
1 AATTA
5470336 GGGTTCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (23 bp):
AATTAAATGAATATATTCAATTA
Found at i:5471613 original size:33 final size:33
Alignment explanation
Indices: 5471551--5471613 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5471541 ACACAATATG
* * *
5471551 GTATTTAAGATATATATATATATGTATATAATA
1 GTATTTAAGATATATATACATAAGAATATAATA
5471584 GTATTTAAGA-ATATATACATAAGAAATATA
1 GTATTTAAGATATATATACATAAG-AATATA
5471614 TAACTAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.40
Consensus pattern (33 bp):
GTATTTAAGATATATATACATAAGAATATAATA
Found at i:5472215 original size:27 final size:26
Alignment explanation
Indices: 5472150--5472214 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
5472140 TTTTTTTGGG
*
5472150 GGGTTACG-TTTTTCTTTTTCTTTTT
1 GGGTTAGGTTTTTTCTTTTTCTTTTT
*
5472175 GGGTTAGGTTTTTTCTTTTTTTTTTT
1 GGGTTAGGTTTTTTCTTTTTCTTTTT
*
5472201 TGGTTAGGTTTTTT
1 GGGTTAGGTTTTTT
5472215 TTTGGGAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 7 0.19
26 29 0.81
ACGTcount: A:0.05, C:0.06, G:0.20, T:0.69
Consensus pattern (26 bp):
GGGTTAGGTTTTTTCTTTTTCTTTTT
Found at i:5473161 original size:72 final size:72
Alignment explanation
Indices: 5473073--5473766 Score: 1037
Period size: 72 Copynumber: 9.5 Consensus size: 72
5473063 GTGATTTGAA
5473073 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
*
5473138 TCCCGAG
66 TCCTGAG
5473145 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
*
5473210 TCCCGAG
66 TCCTGAG
* *
5473217 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAAATTGAAAATACCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG-AAAAC-AGAAATTGAAATTACCTCAG
* *
5473282 CATGTCTTGAG
62 CGTGTCCTGAG
* ** *
5473293 GTTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
5473358 TCCTGAG
66 TCCTGAG
** *
5473365 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA-AACAGAAATTGAAATTACCTCAGCG
5473430 TGTCCTGAG
64 TGTCCTGAG
* * * * *
5473439 GCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAGACAAAAATTAAAAATACCTCAAC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAA-ACAGAAATTGAAATTACCTCAGC
*
5473504 GTGTCTTGAG
63 GTGTCCTGAG
** * *
5473514 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
*
5473579 TCCCGAG
66 TCCTGAG
*
5473586 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
*
5473651 TCCCGAG
66 TCCTGAG
*
5473658 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAATTACCTCAGCG
5473723 TGTCCTGAG
64 TGTCCTGAG
*
5473732 GCTCAACTCACCTCTCGCAGTATGAGTTGATTTTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5473767 TTTGAAACAG
Statistics
Matches: 569, Mismatches: 43, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
72 288 0.51
73 19 0.03
74 141 0.25
75 68 0.12
76 53 0.09
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (72 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
TCCTGAG
Found at i:5473647 original size:293 final size:295
Alignment explanation
Indices: 5473073--5473785 Score: 1102
Period size: 293 Copynumber: 2.4 Consensus size: 295
5473063 GTGATTTGAA
*
5473073 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA-AACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCTCAGCG
* * * * *
5473136 TGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAATT
66 TGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAACAAAAATTAAAAAT
* *
5473199 ACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAA
131 ACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TATTTTGAAAAACAAA
** * **
5473264 AAATTGAAAATACCTCAGCATGTCTTGAGGTTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
195 AAATTGAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG
* *
5473329 AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAG
260 AAAACAGAAATTGAAATTACCTCAGCGTCTCCCGAG
**
5473365 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCTCAGCG
5473430 TGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAGACAAAAATTAAAAA
66 TGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAA-ACAAAAATTAAAAA
** **
5473495 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTG-AAAAC-AA
130 TACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTGAAAAACAAA
* * *
5473557 AAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
195 AAATTGAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG
5473622 AAAACAGAAATTGAAATTACCTCAGCGTCTCCCGAG
260 AAAACAGAAATTGAAATTACCTCAGCGTCTCCCGAG
*
5473658 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCTCAGCG
*
5473723 TGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTTG-AAACAGAAA-TAAAAA
66 TGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGA-TTTTTTTGAAAACAAAAATTAAAAA
5473786 CATCAAAATA
Statistics
Matches: 387, Mismatches: 28, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
291 6 0.02
292 34 0.09
293 203 0.52
294 75 0.19
295 5 0.01
296 9 0.02
297 55 0.14
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (295 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCTCAGCG
TGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAACAAAAATTAAAAAT
ACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTGAAAAACAAAA
AATTGAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA
AAACAGAAATTGAAATTACCTCAGCGTCTCCCGAG
Found at i:5482083 original size:12 final size:12
Alignment explanation
Indices: 5482063--5482098 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5482053 TCGGAGATGC
*
5482063 AATGTATGAATG
1 AATGCATGAATG
5482075 AATGCATGAATG
1 AATGCATGAATG
5482087 AATGCATGAATG
1 AATGCATGAATG
5482099 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:5484640 original size:22 final size:21
Alignment explanation
Indices: 5484615--5484673 Score: 93
Period size: 22 Copynumber: 2.8 Consensus size: 21
5484605 TTTTTTGGGG
5484615 GGTTAGGTTTTCTTTTTCTTTT
1 GGTTAGGTTTTCTTTTT-TTTT
5484637 GGTTAGGTTTTTCTTTTTTTTT
1 GGTTAGG-TTTTCTTTTTTTTT
5484659 GGTTAGGTTTT-TTTT
1 GGTTAGGTTTTCTTTT
5484674 GGAGGCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 18 0.50
23 10 0.28
ACGTcount: A:0.05, C:0.05, G:0.20, T:0.69
Consensus pattern (21 bp):
GGTTAGGTTTTCTTTTTTTTT
Found at i:5487025 original size:14 final size:14
Alignment explanation
Indices: 5487006--5487032 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5486996 TTCTCTTTTG
5487006 CCCTTCCCCTTCCC
1 CCCTTCCCCTTCCC
5487020 CCCTTCCCCTTCC
1 CCCTTCCCCTTCC
5487033 ATTTTACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (14 bp):
CCCTTCCCCTTCCC
Found at i:5490634 original size:31 final size:31
Alignment explanation
Indices: 5490596--5490665 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
5490586 TTTGACTATC
* *
5490596 ATTTTTAAT-AAAATTCTGACTAAAACGTTAA
1 ATTTTTAATGAAAATAC-AACTAAAACGTTAA
* *
5490627 ATTTTTAATGAAAATACAATTAAAATGTTAA
1 ATTTTTAATGAAAATACAACTAAAACGTTAA
5490658 ATTTTTAA
1 ATTTTTAA
5490666 ACATAGCTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (31 bp):
ATTTTTAATGAAAATACAACTAAAACGTTAA
Found at i:5490983 original size:143 final size:143
Alignment explanation
Indices: 5490799--5491082 Score: 428
Period size: 143 Copynumber: 2.0 Consensus size: 143
5490789 ACAAATAATA
*
5490799 TCATATCGAATTAAATTACACATGGACTGTCATACGAGTCACCAAACCAACATCGTTAAAAAATT
1 TCATATCGAATTAAAATACACATGGACTGTCATACGAGTCACCAAACCAACATCGTTAAAAAATT
* ** *
5490864 AATGTTTTAATCGGTCATTTAAAAAAGTGATTTGAA-TCCTTTCAAAAAATTAATGGTCAAATTT
66 AATATTTTAATCAATCATTTAAAAAAGTAATTT-AAGTCCTTTCAAAAAATTAATGGTCAAATTT
5490928 AACTAAAAAATAGT
130 AACTAAAAAATAGT
* *
5490942 TCATATCGACA-TAAAATACACATGGATTGTCATACGAGTCACCAGACCAACATCGTTAAAAAAT
1 TCATATCGA-ATTAAAATACACATGGACTGTCATACGAGTCACCAAACCAACATCGTTAAAAAAT
* ** **
5491006 TAATATTTTAATCAATCATTTAAAAAGGTAATTTAAGTCCTTTTGAAAGGTTAATGGTCAAATTT
65 TAATATTTTAATCAATCATTTAAAAAAGTAATTTAAGTCCTTTCAAAAAATTAATGGTCAAATTT
5491071 AACTAAAAAATA
130 AACTAAAAAATA
5491083 AAGTCAATTT
Statistics
Matches: 127, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
142 2 0.02
143 124 0.98
144 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (143 bp):
TCATATCGAATTAAAATACACATGGACTGTCATACGAGTCACCAAACCAACATCGTTAAAAAATT
AATATTTTAATCAATCATTTAAAAAAGTAATTTAAGTCCTTTCAAAAAATTAATGGTCAAATTTA
ACTAAAAAATAGT
Found at i:5495341 original size:21 final size:21
Alignment explanation
Indices: 5495315--5495354 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5495305 TCATGCCAAG
*
5495315 CAGATTAGAACTCACCTGAGC
1 CAGATTAAAACTCACCTGAGC
5495336 CAGATTAAAACTCACCTGA
1 CAGATTAAAACTCACCTGA
5495355 ATTCATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.20
Consensus pattern (21 bp):
CAGATTAAAACTCACCTGAGC
Found at i:5503542 original size:40 final size:40
Alignment explanation
Indices: 5503487--5503564 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 40
5503477 TACGGTACCT
5503487 TTTGGTGTGTAGGGTTG-GATGGGTTGATTATATCCCCATG
1 TTTGGTGTGTAGGGTTGAG-TGGGTTGATTATATCCCCATG
*
5503527 TTTGGTGTGTAGGGTTGAGTGGGTTGATTCTATCCCCA
1 TTTGGTGTGTAGGGTTGAGTGGGTTGATTATATCCCCA
5503565 CATGGTGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.14, C:0.12, G:0.35, T:0.40
Consensus pattern (40 bp):
TTTGGTGTGTAGGGTTGAGTGGGTTGATTATATCCCCATG
Found at i:5503580 original size:38 final size:39
Alignment explanation
Indices: 5503489--5503582 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 39
5503479 CGGTACCTTT
**
5503489 TGGTGTGTAGGGTTGGATGGGTTGATTATATCCCCATGTT
1 TGGTGTGTAGGGTTGGATGGGTTGATTATATCCCCA-GCA
*
5503529 TGGTGTGTAGGGTT-GAGTGGGTTGATTCTATCCCCA-CA
1 TGGTGTGTAGGGTTGGA-TGGGTTGATTATATCCCCAGCA
*
5503567 TGGTGTGTTGGGTTGG
1 TGGTGTGTAGGGTTGG
5503583 TTGGAGATAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 13 0.27
39 3 0.06
40 32 0.67
ACGTcount: A:0.13, C:0.11, G:0.38, T:0.38
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGATGGGTTGATTATATCCCCAGCA
Found at i:5512241 original size:17 final size:17
Alignment explanation
Indices: 5512219--5512269 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
5512209 GCATAAACAA
5512219 TCTTTTATAAAAAAATT
1 TCTTTTATAAAAAAATT
* *
5512236 TCTTTTAT-GAATAATT
1 TCTTTTATAAAAAAATT
*
5512252 TCATTTTATATAAAAATT
1 TC-TTTTATAAAAAAATT
5512270 AATTTGAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 8 0.29
17 14 0.50
18 6 0.21
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (17 bp):
TCTTTTATAAAAAAATT
Found at i:5512847 original size:47 final size:47
Alignment explanation
Indices: 5512778--5512869 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
5512768 TATCACTATT
*
5512778 CACTCTCATATACATAATATATGTAATTTAAATTAAGTTTAATTATC
1 CACTCTCATATACATAATATATGTAATTTAAATCAAGTTTAATTATC
5512825 CACTCTCATATACATAATATATGTAATTTAAATCAAGTTTAATTA
1 CACTCTCATATACATAATATATGTAATTTAAATCAAGTTTAATTA
5512870 GGTATTATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (47 bp):
CACTCTCATATACATAATATATGTAATTTAAATCAAGTTTAATTATC
Found at i:5515022 original size:21 final size:21
Alignment explanation
Indices: 5514993--5515033 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5514983 TTTATGTTAT
* *
5514993 AAATTACATAATATTATATAA
1 AAATAACATAATATAATATAA
5515014 AAATAACATAATATAATATA
1 AAATAACATAATATAATATA
5515034 TTACAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATAACATAATATAATATAA
Found at i:5516593 original size:19 final size:18
Alignment explanation
Indices: 5516545--5516579 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5516535 CAATAAGATA
*
5516545 ATTATATTTAAAAAATAC
1 ATTAAATTTAAAAAATAC
5516563 ATTAAATTTAAAAAATA
1 ATTAAATTTAAAAAATA
5516580 ACTCTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTAAATTTAAAAAATAC
Found at i:5537434 original size:15 final size:15
Alignment explanation
Indices: 5537414--5537443 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5537404 TCGAGGAAGC
5537414 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
*
5537429 AAAAAAAGAAAAAGA
1 AAAAAAAAAAAAAGA
5537444 CAACCATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:5538358 original size:17 final size:17
Alignment explanation
Indices: 5538338--5538373 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5538328 GGAAGCTAAG
5538338 GATTCTTGGATAACGTA
1 GATTCTTGGATAACGTA
*
5538355 GATTCTTGGATAATGTA
1 GATTCTTGGATAACGTA
5538372 GA
1 GA
5538374 GGTGTTCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (17 bp):
GATTCTTGGATAACGTA
Found at i:5542060 original size:27 final size:27
Alignment explanation
Indices: 5541945--5542051 Score: 171
Period size: 27 Copynumber: 4.0 Consensus size: 27
5541935 TAACTTAGGC
* * *
5541945 AATATGAAAGGAACA-CCTTTATGGTGT
1 AATATGAAA-GAAAAGCCTTTGTGGCGT
5541972 AATATGAAAGAAAAGCCTTTGTGGCGT
1 AATATGAAAGAAAAGCCTTTGTGGCGT
5541999 AATATGAAAGAAAAGCCTTTGTGGCGT
1 AATATGAAAGAAAAGCCTTTGTGGCGT
5542026 AATATGAAAGAAAAGCCTTTGTGGCG
1 AATATGAAAGAAAAGCCTTTGTGGCG
5542052 AACTCTGAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 4 0.05
27 72 0.95
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.26
Consensus pattern (27 bp):
AATATGAAAGAAAAGCCTTTGTGGCGT
Found at i:5544602 original size:6 final size:6
Alignment explanation
Indices: 5544591--5544656 Score: 125
Period size: 6 Copynumber: 11.2 Consensus size: 6
5544581 TCTTAAGCTT
5544591 TAAAAA TAAAAA TAAAAA TAAAAA T-AAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
5544638 TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA T
5544657 GGGGAAGATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.08
6 54 0.92
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:5552347 original size:42 final size:42
Alignment explanation
Indices: 5552301--5552422 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
5552291 TCCAACACTA
*
5552301 TTTCCTGACTGACCT-CCATTTCC-GATACCAAATCCAATACCG
1 TTTCCTAACTG-CCTCCCATTTCCAG-TACCAAATCCAATACCG
** *
5552343 TTTCCTAACTGGTTCCCATTTCCAGTACCATATCCAATACCCG
1 TTTCCTAACTGCCTCCCATTTCCAGTACCAAATCCAATA-CCG
** * *
5552386 -TTCCTAACTGGTTCCCATTTCCAGTGCCATATCCAAT
1 TTTCCTAACTGCCTCCCATTTCCAGTACCAAATCCAAT
5552423 GCCATATCCC
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
41 1 0.01
42 67 0.93
43 4 0.06
ACGTcount: A:0.24, C:0.34, G:0.10, T:0.32
Consensus pattern (42 bp):
TTTCCTAACTGCCTCCCATTTCCAGTACCAAATCCAATACCG
Found at i:5552635 original size:42 final size:44
Alignment explanation
Indices: 5552543--5552643 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 44
5552533 GATCCCCATT
* *
5552543 TCCAATGCCATACCCAATGCCCATCCCTAACTGGTTCCCACTTC
1 TCCAATGCCATATCCAATGCCCATACCTAACTGGTTCCCACTTC
* ** *
5552587 -CC-ATGCCATGTCCAATGCCTGTACCTACCTGGTT-CC-CTTC
1 TCCAATGCCATATCCAATGCCCATACCTAACTGGTTCCCACTTC
5552627 TCCAATGCCATATCCAA
1 TCCAATGCCATATCCAA
5552644 CGCCATATCC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
40 4 0.08
41 4 0.08
42 38 0.79
43 2 0.04
ACGTcount: A:0.22, C:0.41, G:0.11, T:0.27
Consensus pattern (44 bp):
TCCAATGCCATATCCAATGCCCATACCTAACTGGTTCCCACTTC
Found at i:5552703 original size:54 final size:54
Alignment explanation
Indices: 5552585--5552703 Score: 166
Period size: 54 Copynumber: 2.2 Consensus size: 54
5552575 GGTTCCCACT
* * *
5552585 TCCCATGCCATGTCCAATGCCTGTACCTACCTGGTTCCCTTCTCCAATGCCATA
1 TCCCATGCCATATCCAATGCCTGTACCTAACTGGTTCCCATCTCCAATGCCATA
* * * * *
5552639 TCCAACGCCATATCCAGTGGCTGTACCTAACTGGTTCCCATCTTCAATGCCATA
1 TCCCATGCCATATCCAATGCCTGTACCTAACTGGTTCCCATCTCCAATGCCATA
5552693 TCCCATGCCAT
1 TCCCATGCCAT
5552704 TTCCTGAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.21, C:0.37, G:0.13, T:0.29
Consensus pattern (54 bp):
TCCCATGCCATATCCAATGCCTGTACCTAACTGGTTCCCATCTCCAATGCCATA
Found at i:5552950 original size:15 final size:17
Alignment explanation
Indices: 5552925--5552957 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5552915 CGGTAACGGC
5552925 ACTGTCCGAAA-CCGCT
1 ACTGTCCGAAACCCGCT
5552941 ACTG-CCGAAACCCGCT
1 ACTGTCCGAAACCCGCT
5552957 A
1 A
5552958 TACCCGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
ACTGTCCGAAACCCGCT
Found at i:5557729 original size:38 final size:38
Alignment explanation
Indices: 5557669--5557752 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
5557659 ATTTGATGTG
* * * *
5557669 TATTCGGGTTAAATCCTACAGGCTTCGTGCTGGTATTA
1 TATTCGGGATAAATCCCACAGGCCTAGTGCTGGTATTA
* *
5557707 TATTTGGGATAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATTCGGGATAAATCCCACAGGCCTAGTGCTGGTATTA
5557745 TATTCGGG
1 TATTCGGG
5557753 CCTTTGTGCC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (38 bp):
TATTCGGGATAAATCCCACAGGCCTAGTGCTGGTATTA
Found at i:5576828 original size:3 final size:3
Alignment explanation
Indices: 5576820--5576856 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5576810 ATTTGACTTC
5576820 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5576857 CACAATTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5577194 original size:171 final size:167
Alignment explanation
Indices: 5576847--5577251 Score: 467
Period size: 170 Copynumber: 2.4 Consensus size: 167
5576837 TTATTATTAT
* * *
5576847 TATTATTATTCACAATTATCAT-TTTTCTTGTCGAAATTAGGATGTCCACTATCGGTAGCAATGA
1 TATTATTATTCACAATTATCATATTTTTTTCTCGAAATTAGGATGTCCACTACCGGTAGCAATGA
* * * *
5576911 TTAATTCCCTCGTTTGTCTCCAACTTGGACAAATATAGAAATAAAAATCAAAGGGTCCCACTCCC
66 CTAATCCCCTCGTGTGTCTCCAACTTGGACAAATATAGAAACAAAAATCAAAGGGTCCCACTCCC
* *
5576976 AACACTTCCAAAAATATTCAAATATGACTATTCAAAG
131 AACACTACCAAAAATATTCAAATATGACTACTCAAAG
* * * *
5577013 TATCATTATTCACAATTATTCATATTTTTTTCTCTTGAAATTAGGATGTCTATTGCCGGTAGCAA
1 TATTATTATTCACAATTA-TCATATTTTTTTCTC--GAAATTAGGATGTCCACTACCGGTAGCAA
* * *
5577078 TGACTAATCCCCTCGTGTG-CTTCCAACTTGGACAAATGTCA-AAGCAAATATCAAAGGGTTCCC
63 TGACTAATCCCCTCGTGTGTC-TCCAACTTGGACAAATAT-AGAAACAAAAATCAAAGGG-TCCC
* *** *
5577141 ACTCCCAACGCTACTTGAAATATTCAAATTTGACTACTCAAAG
125 ACTCCCAACACTACCAAAAATATTCAAATATGACTACTCAAAG
* * * * ** *
5577184 TATTATTATTCACAATCATCAATATTTTTTT-TCCAAATTAGAATGTCCATTATTGGTAGTAATG
1 TATTATTATTCACAATTATC-ATATTTTTTTCTCGAAATTAGGATGTCCACTACCGGTAGCAATG
5577248 ACTA
65 ACTA
5577252 GTTCCATCGT
Statistics
Matches: 201, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
166 17 0.08
167 4 0.02
168 36 0.18
169 1 0.00
170 76 0.38
171 67 0.33
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (167 bp):
TATTATTATTCACAATTATCATATTTTTTTCTCGAAATTAGGATGTCCACTACCGGTAGCAATGA
CTAATCCCCTCGTGTGTCTCCAACTTGGACAAATATAGAAACAAAAATCAAAGGGTCCCACTCCC
AACACTACCAAAAATATTCAAATATGACTACTCAAAG
Found at i:5587128 original size:25 final size:25
Alignment explanation
Indices: 5587096--5587152 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
5587086 TTCACTATAG
*
5587096 TTTCAGAGGATGCTAACTATAGTAT
1 TTTCAGAGGATGCTAACTACAGTAT
* *
5587121 TTTCAGAGTATGCTATCTACAGTAT
1 TTTCAGAGGATGCTAACTACAGTAT
5587146 TTTCAGA
1 TTTCAGA
5587153 ATAAACTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (25 bp):
TTTCAGAGGATGCTAACTACAGTAT
Found at i:5587164 original size:25 final size:25
Alignment explanation
Indices: 5587116--5587164 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5587106 TGCTAACTAT
* **
5587116 AGTATTTTCAGAGTATGCTATCTAC
1 AGTATTTTCAGAATAAACTATCTAC
*
5587141 AGTATTTTCAGAATAAACTGTCTA
1 AGTATTTTCAGAATAAACTATCTA
5587165 AACTTCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (25 bp):
AGTATTTTCAGAATAAACTATCTAC
Found at i:5587943 original size:34 final size:34
Alignment explanation
Indices: 5587905--5587970 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
5587895 GTTTCAGTTA
*
5587905 GGGCCTTAGCCCATTACAGTATCGGTATCAGTGT
1 GGGCCTTAGCCCATTACAGTATCGGTAACAGTGT
* *
5587939 GGGCCTTAGCCCATTTCAGTGTCGGTAACAGT
1 GGGCCTTAGCCCATTACAGTATCGGTAACAGT
5587971 ACAGATATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (34 bp):
GGGCCTTAGCCCATTACAGTATCGGTAACAGTGT
Found at i:5591852 original size:6 final size:6
Alignment explanation
Indices: 5591836--5591865 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5591826 AAAAGGAGAA
*
5591836 TAAAAT AAAAAT TAAAAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
5591866 GAAATTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TAAAAT
Found at i:5599855 original size:20 final size:21
Alignment explanation
Indices: 5599827--5599865 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5599817 TCTATAATTA
5599827 CTATATCACATTG-TTTCTTC
1 CTATATCACATTGATTTCTTC
* *
5599847 CTATTTCACTTTGATTTCT
1 CTATATCACATTGATTTCT
5599866 CAAAACCGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.54
Consensus pattern (21 bp):
CTATATCACATTGATTTCTTC
Found at i:5604153 original size:5 final size:6
Alignment explanation
Indices: 5604137--5604193 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
5604127 TTGTTTACAT
* * *
5604137 TAAAAA TAAAAA TAAAAA TAAAAA TCAAGGAGA CAAAAA GTAAAAA GAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA T-AA--AAA TAAAAA -TAAAAA TAAAAA
5604189 TAAAA
1 TAAAA
5604194 GCATGTGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
6 30 0.73
7 7 0.17
8 2 0.05
9 2 0.05
ACGTcount: A:0.75, C:0.04, G:0.09, T:0.12
Consensus pattern (6 bp):
TAAAAA
Found at i:5605100 original size:23 final size:23
Alignment explanation
Indices: 5605072--5605165 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
5605062 ATGTGTGTAT
* *
5605072 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGTCTCTTCA
*
5605095 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
* * *
5605118 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTCTTCA
5605141 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
5605164 CT
1 CT
5605166 CTTCTAACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTCTTCA
Found at i:5609607 original size:23 final size:23
Alignment explanation
Indices: 5609579--5609671 Score: 132
Period size: 23 Copynumber: 4.0 Consensus size: 23
5609569 ATGTGTGTAT
* *
5609579 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGTCTCTTCA
*
5609602 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
* * *
5609625 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTCTTCA
5609648 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
5609671 C
1 C
5609672 ACTTCTAACT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.23, C:0.26, G:0.04, T:0.47
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTCTTCA
Found at i:5614209 original size:7 final size:6
Alignment explanation
Indices: 5614198--5614222 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5614188 TTGTTTAAAT
5614198 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
5614223 CAAGGAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:5631313 original size:43 final size:43
Alignment explanation
Indices: 5631265--5631548 Score: 505
Period size: 43 Copynumber: 6.6 Consensus size: 43
5631255 CCGGCATTAC
*
5631265 GCCTGCTAGGCATGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5631308 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCAAGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5631351 GCCTGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5631394 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGACACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5631437 GCCTGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5631480 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5631523 GCCTGCTAGGCACGAAGGCCCAAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
5631549 TAATACCAGC
Statistics
Matches: 230, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 230 1.00
ACGTcount: A:0.31, C:0.33, G:0.25, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:5631589 original size:38 final size:38
Alignment explanation
Indices: 5631546--5631648 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
5631536 GAAGGCCCAA
* * * *
5631546 ATATAATACCAGCACTAGGCCTGCGGGATTTATCCCTG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
5631584 ATATAATACCAACACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
**
5631622 ATATTTTACCAGCACGAAGCCTGCGGG
1 ATATAATACCAGCACGAAGCCTGCGGG
5631649 TCTTTAAGCC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:5635296 original size:12 final size:12
Alignment explanation
Indices: 5635276--5635398 Score: 82
Period size: 12 Copynumber: 10.5 Consensus size: 12
5635266 TCTTAAAATT
5635276 ATAAATAATATA
1 ATAAATAATATA
*
5635288 ATGAATAATATA
1 ATAAATAATATA
*
5635300 A-ACATAA-ATA
1 ATAAATAATATA
5635310 ATATAATAA-ATA
1 ATA-AATAATATA
* *
5635322 ATATATGATATA
1 ATAAATAATATA
5635334 CAT-AATATATGATA
1 -ATAAATA-AT-ATA
*
5635348 AAAAATAATATA
1 ATAAATAATATA
*
5635360 ATAAGTAATAT-
1 ATAAATAATATA
5635371 ATATAATAA-A-A
1 ATA-AATAATATA
*
5635382 GTAAA-AATATA
1 ATAAATAATATA
5635393 ATAAAT
1 ATAAAT
5635399 GCTATATAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
9 2 0.02
10 7 0.08
11 19 0.22
12 43 0.51
13 7 0.08
14 7 0.08
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (12 bp):
ATAAATAATATA
Found at i:5635324 original size:7 final size:7
Alignment explanation
Indices: 5635271--5635380 Score: 51
Period size: 7 Copynumber: 14.4 Consensus size: 7
5635261 ACAAATCTTA
*
5635271 AAATTAT
1 AAATAAT
5635278 AAATAAT
1 AAATAAT
5635285 ATAATGAAT
1 A-AAT-AAT
5635294 AATATAA-
1 AA-ATAAT
*
5635301 ACATAAAT
1 AAAT-AAT
5635309 AATATAAT
1 AA-ATAAT
5635317 AAATAAT
1 AAATAAT
*
5635324 ATATGATAT
1 AAAT-A-AT
*
5635333 ACATAAT
1 AAATAAT
* *
5635340 ATATGAT
1 AAATAAT
*
5635347 AAAAAAT
1 AAATAAT
5635354 AATATAAT
1 AA-ATAAT
*
5635362 AAGTAAT
1 AAATAAT
5635369 ATATATAAT
1 A-A-ATAAT
5635378 AAA
1 AAA
5635381 AGTAAAAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 22
0.69 0.11 0.19
Matches are distributed among these distances:
6 2 0.03
7 37 0.47
8 22 0.28
9 18 0.23
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (7 bp):
AAATAAT
Found at i:5635371 original size:38 final size:38
Alignment explanation
Indices: 5635278--5635395 Score: 92
Period size: 38 Copynumber: 3.2 Consensus size: 38
5635268 TTAAAATTAT
*
5635278 AAATAATATAATGAA-TAATATAAACATAA-ATAAT-ATAAT
1 AAATAATATAAT-AAGTAATAT--ACATAATAT-ATGATAAA
5635317 AAATAATAT-AT--G--ATATACATAATATATGATAAA
1 AAATAATATAATAAGTAATATACATAATATATGATAAA
* * *
5635350 AAATAATATAATAAGTAATATATATAATAAAAG-TAAA
1 AAATAATATAATAAGTAATATACATAATATATGATAAA
5635387 AATATAATA
1 AA-ATAATA
5635396 AATGCTATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
32 8 0.12
33 15 0.23
34 6 0.09
36 1 0.02
37 6 0.09
38 21 0.32
39 9 0.14
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (38 bp):
AAATAATATAATAAGTAATATACATAATATATGATAAA
Found at i:5635376 original size:16 final size:15
Alignment explanation
Indices: 5635285--5635379 Score: 69
Period size: 16 Copynumber: 6.3 Consensus size: 15
5635275 TATAAATAAT
5635285 ATAATGAATA-ATATA
1 ATAAT-AATATATATA
5635300 A-ACATAA-ATAATATA
1 ATA-ATAATAT-ATATA
5635315 ATAAATAATATATGAT-
1 AT-AATAATATAT-ATA
5635331 ATACATAATATATGATA
1 ATA-ATAATATAT-ATA
5635348 A-AA-AATA-ATATA
1 ATAATAATATATATA
5635360 ATAAGTAATATATATA
1 ATAA-TAATATATATA
5635376 ATAA
1 ATAA
5635380 AAGTAAAAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
12 4 0.06
13 5 0.07
14 7 0.10
15 15 0.22
16 30 0.45
17 6 0.09
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
ATAATAATATATATA
Found at i:5635393 original size:17 final size:17
Alignment explanation
Indices: 5635348--5635397 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
5635338 ATATATGATA
5635348 AAAAATA-ATATAATAAGT
1 AAAAATATA-ATAA-AAGT
*
5635366 AATATATATAATAAAAGT
1 AA-AAATATAATAAAAGT
5635384 AAAAATATAATAAA
1 AAAAATATAATAAA
5635398 TGCTATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 11 0.39
18 8 0.29
19 8 0.29
20 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (17 bp):
AAAAATATAATAAAAGT
Found at i:5635406 original size:33 final size:31
Alignment explanation
Indices: 5635338--5635398 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
5635328 GATATACATA
* * *
5635338 ATATATGATAAAAAATAATATAATAAGTAAT
1 ATATATAATAAAAAAAAATATAATAAATAAT
5635369 ATATATAATAAAAGTAAAAATATAATAAAT
1 ATATATAATAAAA--AAAAATATAATAAAT
5635399 GCTATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.48
33 13 0.52
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (31 bp):
ATATATAATAAAAAAAAATATAATAAATAAT
Found at i:5635421 original size:17 final size:17
Alignment explanation
Indices: 5635369--5635425 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
5635359 AATAAGTAAT
5635369 ATATATAATAAAAGTA-A
1 ATATATAATAAAA-TACA
* *
5635386 AAATATAAT-AAATGC-
1 ATATATAATAAAATACA
5635401 -TATATAATAAAATACA
1 ATATATAATAAAATACA
5635417 ATATA-AATA
1 ATATATAATA
5635426 TATATAGGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 7 0.22
15 6 0.19
16 7 0.22
17 12 0.38
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (17 bp):
ATATATAATAAAATACA
Found at i:5635519 original size:23 final size:24
Alignment explanation
Indices: 5635475--5635519 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
5635465 TCAATAGTAT
*
5635475 TTTTAATAATAATATATGTATAGA
1 TTTTAATAATAATAAATGTATAGA
5635499 TTTTAA-AATAAATAAAT-TATA
1 TTTTAATAAT-AATAAATGTATA
5635520 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
TTTTAATAATAATAAATGTATAGA
Found at i:5635526 original size:20 final size:18
Alignment explanation
Indices: 5635503--5635553 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
5635493 TATAGATTTT
*
5635503 AAAATAAATAAATTATATAA
1 AAAATAAAAAAATT-TA-AA
5635523 AAAATAAAAAAATTTAAA
1 AAAATAAAAAAATTTAAA
*
5635541 ATAATAAAGAAAA
1 AAAATAAA-AAAA
5635554 GGAGTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.32
19 6 0.21
20 13 0.46
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATAAAAAAATTTAAA
Found at i:5643846 original size:51 final size:52
Alignment explanation
Indices: 5643758--5643859 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 52
5643748 TTTTTTTAAA
* *
5643758 TCTGATAAAGTTGGTGTCGGCCTTCAATGTCCCAAAAC-TAAAAAAATTTAT
1 TCTGATAAAGTTGGTGCCGGCCTTCAATGTCCCAAAACAAAAAAAAATTTAT
*
5643809 TCTGATAAAGTTGGTGCCGG-CTATCAGTG-CCCTAAAACAAAAAAAAATTTA
1 TCTGATAAAGTTGGTGCCGGCCT-TCAATGTCCC-AAAACAAAAAAAAATTTA
5643860 ATAAAGTTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
50 5 0.11
51 29 0.64
52 11 0.24
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TCTGATAAAGTTGGTGCCGGCCTTCAATGTCCCAAAACAAAAAAAAATTTAT
Found at i:5644389 original size:82 final size:81
Alignment explanation
Indices: 5644231--5644392 Score: 225
Period size: 82 Copynumber: 2.0 Consensus size: 81
5644221 GTTTACTCAT
* * ***
5644231 TTCCCACTTGATTCTGTTTCTTGTCACATCACCTCGCATGCGCCAACATATTTCAATTTTTTTGC
1 TTCCCACTTGATTCTGTTTCTTGTCACATCACCCCACATGCGCCAACATATTTCAAAACTTTTGC
*
5644296 TTTTCACTTAAGTAAA
66 TTTCCACTTAAGTAAA
* **
5644312 TTCCCACTTGATTTTGTTTCTTGTCACATCACCCCTACATGCGCGTACATATTTCAAAACTTTTG
1 TTCCCACTTGATTCTGTTTCTTGTCACATCACCCC-ACATGCGCCAACATATTTCAAAACTTTTG
*
5644377 CTTTCCATTTAAGTAA
65 CTTTCCACTTAAGTAA
5644393 TTGACTAACT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
81 33 0.47
82 37 0.53
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.41
Consensus pattern (81 bp):
TTCCCACTTGATTCTGTTTCTTGTCACATCACCCCACATGCGCCAACATATTTCAAAACTTTTGC
TTTCCACTTAAGTAAA
Found at i:5644899 original size:103 final size:103
Alignment explanation
Indices: 5644696--5644943 Score: 297
Period size: 103 Copynumber: 2.4 Consensus size: 103
5644686 ACAAAAATAT
* * ** ** *
5644696 CAGTATTTTAAAAAAATCAGTTCTGGCCTGTCAATGGCAAGCACCAAGTACGAAAAAAATAAATT
1 CAGTATTTAAAAAAAATTAGAGCTGGCCTGTCAATGGCCGGCACCAAGTACAAAAAAAATAAATT
5644761 TTTTTGTGCTGGCCTGTCAATGGTCGACACCAGAGTA-
66 TTTTTGTGCTGGCCTGTCAATGGTCGACACCAGAGTAC
* * *
5644798 C-GTATTTTAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCAAGTACAAAAAAAAT-C
1 CAGTA-TTT-AAAAAAAA-TTAGAGCTGGCCTGTCAATGGCCGGCACCAAGTACAAAAAAAATAA
* * * *
5644861 ATTTTTTTGTGTTGGTCTGTTAATGGAT-GGCACCAGAGTAC
63 ATTTTTTTGTGCTGGCCTGTCAATGG-TCGACACCAGAGTAC
*
5644902 CAGTATTTAAAAAAAATTAGAGCTGGCTTGTCAATGGCCGGC
1 CAGTATTTAAAAAAAATTAGAGCTGGCCTGTCAATGGCCGGC
5644944 TCCAGACTTA
Statistics
Matches: 125, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
101 3 0.02
102 27 0.22
103 49 0.39
104 43 0.34
105 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (103 bp):
CAGTATTTAAAAAAAATTAGAGCTGGCCTGTCAATGGCCGGCACCAAGTACAAAAAAAATAAATT
TTTTTGTGCTGGCCTGTCAATGGTCGACACCAGAGTAC
Found at i:5648034 original size:76 final size:76
Alignment explanation
Indices: 5647957--5648167 Score: 266
Period size: 76 Copynumber: 2.8 Consensus size: 76
5647947 AAAGGTTGAT
** * *
5647957 AATTTAAATGAAATGAGAAAACAATTTTGTTTGAAATGAAATG-GTACAAAATTTAAATGAAAAT
1 AATTTAAATGAAATGAGAAAACAA-TTTCATTGAAATGAAATGAG-AAAAAAATTAAATGAAAAT
5648021 TGAAAGAAAGATA
64 TGAAAGAAAGATA
* *
5648034 AATTTAAATGAAATGAGGAAAA-AATTTCATTGAAATGAAATGAGAAAAAAATTAAATTAAATTT
1 AATTTAAATGAAATGA-GAAAACAATTTCATTGAAATGAAATGAGAAAAAAATTAAATGAAAATT
5648098 GAAAGAAAGATA
65 GAAAGAAAGATA
* * * * *
5648110 AATTTAAATGAAATGAGAGAAAC-TTTTAATTTAAATAAAATGAGCAAAAAATTAAATG
1 AATTTAAATGAAATGAGA-AAACAATTTCATTGAAATGAAATGAGAAAAAAATTAAATG
5648168 GAAAGATAGA
Statistics
Matches: 118, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
75 2 0.02
76 92 0.78
77 19 0.16
78 5 0.04
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.28
Consensus pattern (76 bp):
AATTTAAATGAAATGAGAAAACAATTTCATTGAAATGAAATGAGAAAAAAATTAAATGAAAATTG
AAAGAAAGATA
Found at i:5648210 original size:48 final size:47
Alignment explanation
Indices: 5648157--5648262 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 47
5648147 AAATGAGCAA
*
5648157 AAAATTAAATGGAAAGATAGATAATTTAAAAGAAATGACA-AAAAAAATT
1 AAAATTAAATGGAAA-ATAGAAAATTTAAAAGAAAT-A-AGAAAAAAATT
* ** * *
5648206 AAATTTGCATTGAAAATAGAAAATTTAAATGAAATAAGAAAAAAATT
1 AAAATTAAATGGAAAATAGAAAATTTAAAAGAAATAAGAAAAAAATT
5648253 AAAATTAAAT
1 AAAATTAAAT
5648263 TTAAAAGTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
46 1 0.02
47 17 0.36
48 18 0.38
49 11 0.23
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.25
Consensus pattern (47 bp):
AAAATTAAATGGAAAATAGAAAATTTAAAAGAAATAAGAAAAAAATT
Found at i:5648296 original size:22 final size:21
Alignment explanation
Indices: 5648243--5648332 Score: 65
Period size: 22 Copynumber: 4.2 Consensus size: 21
5648233 AATGAAATAA
* * *
5648243 GAAAAAAATTAAAATTAAATT
1 GAAAAAAAATATAATTGAATT
* ** *
5648264 TAAAAGTAATATAAATGAATT
1 GAAAAAAAATATAATTGAATT
*
5648285 GAGAAAAAAATA-AATTTAAATT
1 GA-AAAAAAATATAA-TTGAATT
*
5648307 GAAAAAAATATATAATTGAAAT
1 GAAAAAAA-ATATAATTGAATT
5648329 GAAA
1 GAAA
5648333 TGGAAATGGA
Statistics
Matches: 51, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
21 23 0.45
22 26 0.51
23 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (21 bp):
GAAAAAAAATATAATTGAATT
Found at i:5648315 original size:16 final size:18
Alignment explanation
Indices: 5648291--5648327 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5648281 AATTGAGAAA
*
5648291 AAAATAAATTTA-AATTG
1 AAAATAAATATATAATTG
5648308 AAAA-AAATATATAATTG
1 AAAATAAATATATAATTG
5648325 AAA
1 AAA
5648328 TGAAATGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATAAATATATAATTG
Found at i:5648320 original size:44 final size:44
Alignment explanation
Indices: 5648197--5648328 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 44
5648187 AGAAATGACA
** *
5648197 AAAAAAATTAAATTTGCATTGAAAATAGAAAATTTAAATGAAATAAG
1 AAAAAAATTAAATTTAAATTG-AAA-A-AAAATATAAATGAAATAAG
* * ** * *
5648244 AAAAAAATTAAAATTAAATTTAAAAGTAATATAAATGAATTGAG
1 AAAAAAATTAAATTTAAATTGAAAAAAAATATAAATGAAATAAG
*
5648288 AAAAAAA-TAAATTTAAATTGAAAAAAATATATAATTGAAAT
1 AAAAAAATTAAATTTAAATTGAAAAAAA-ATATAAATGAAAT
5648329 GAAATGGAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
43 16 0.23
44 32 0.46
45 1 0.01
46 3 0.04
47 17 0.25
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (44 bp):
AAAAAAATTAAATTTAAATTGAAAAAAAATATAAATGAAATAAG
Done.